Structural analysis of SNARE motifs from sea perch, Lateolabrax japonicus by computerized approaches

Three cDNA sequences encoding four SNARE (N-ethylmaleimide-sensitive fusion protein attachment protein receptors) motifs were cloned from sea perch, and the deduced peptide sequences were analyzed for structural prediction by using 14 different web servers and softwares. The "ionic layer" structure, the three dimensional extension and conformational characters of the SNARE 7S core complex by using bioinformatics approaches were compared respectively with those from mammalian X-ray crystallographic investigations. The result suggested that the formation and stabilization of fish SNARE core complex might be driven by hydrophobic association, hydrogen bond among R group of core amino acids and electrostatic attraction at molecular level. This revealed that the SNARE proteins interaction of the fish may share the same molecular mechanism with that of mammal, indicating the universality and solidity of SNARE core complex theory. This work is also an attempt to get the protein 3D structural information which appears to be similar to that obtained through X-ray crystallography, only by using computerized approaches. (C) 2007 Elsevier Ltd. All rights reserved.

蛇形机器人步态转换CPG控制器

蛇具有细长无肢的身体、独特的半球型关节,使其可在神经系统控制下完成与环境相适应的多种节律运动.基于对该节律运动机制的分析,给出蛇运动神经系统的主要功能特性.首次应用双向循环抑制CPG模拟蛇节律运动发生机制,控制蛇形机器人组合关节,实现3种典型运动.通过单向激励串联该类CPG构成神经网络,给出该神经网络产生振荡输出的必要条件.用不同高级控制神经元命令激活下的输出,实现蛇形机器人典型运动模式的自动转换.通过动力学仿真和实验验证该CPG控制器产生不同节律运动模式的有效性.为蛇节律运动模式发生机制建模提供新方法.

基于循环抑制CPG模型控制的蛇形机器人三维运动

具有三维运动能力和独特的节律运动方式,使生物蛇能在复杂的地形环境中生存.大多数动物节律运动是由中央模式发生器(Centralpatterngenerator,CPG)控制的.以此为理论依据,首次以循环抑制建模机理构建蛇形机器人组合关节运动控制的CPG模型.证明该模型是节律输出型CPG中微分方程维数最少的.采用单向激励方式连接该类CPG构建蛇形机器人三维运动神经网络控制体系,给出该CPG网络产生振荡输出的必要条件.应用蛇形机器人动力学模型仿真得到控制三维运动的CPG神经网络参数,利用该CPG网络的输出使“勘查者”成功实现三维运动.该结果为建立未探明的生物蛇神经网络模型提供了一种全新的方法.

基于循环抑制CPG模型的蛇形机器人控制器

依据生物利用中央模式发生器(Central pattern generator,CPG)的自激行为产生有节律的协调运动适应多种环境,基于循环抑制CPG建模理论设计了蛇形机器人CPG控制器模型,分析了单个神经元、循环抑制CPG以及该控制器模型的稳定性,并把该控制器应用到一个结合蛇形机器人“勘查者-Ⅰ”动力学特性的仿真模型,得到了实现蜿蜒运动的CPG控制器参数,进而研究了调节S波个数、身体构形曲率、蜿蜒运动速度以及运动轨迹曲率的CPG控制器参数设定策略。此外,“勘查者-Ⅰ”应用该CPG控制器的输出成功实现了蜿蜒运动。该研究结果为设计人工CPG控制器提供了一个可行的方法。

基于循环抑制CPG模型控制的蛇形机器人蜿蜒运动

根据生物蛇和蛇形机器人的结构及运动特点,应用循环抑制CPG建模理论构建了蛇形机器人神经网络模型;利用蛇形机器人模型,仿真验证了CPG模型对蜿蜒运动控制的有效性;提出并验证了实现有目的转弯控制的CPG参数调节方法．最后,给出了今后的研究方向．

基于循环抑制CPG的蛇形机器人运动控制方法

蛇具有细长无肢的身体、独特的半球形关节，使其可在神经系统控制下完成与环境相适应的多种节律运动。模仿蛇的运动机理和行为方式而设计的蛇形机器人克服了轮腿式机器人的缺点，增加了机器人的运动方式，扩大了机器人的应用范围。但应用传统的控制策略实现蛇形机器人运动控制遇到了很难克服的问题。随着社会经济与科技的发展，研究人员把从蛇运动神经系统研究中得到的启示应用到蛇形机器人上，希望不仅可以解决其运动控制问题，更能在构型、步态及控制机制上皆可展示蛇的特征。 生物学家已经证明动物的节律运动是其低级神经中枢的自激行为，是由中枢模式发生器(Central Pattern Generator，CPG)控制的。中枢模式发生器是一种能够在缺乏有规律的感知和中枢控制输入的情况下，产生有节奏模式输出的神经网络。 本文以国家自然科学基金课题《基于CPG的蛇形机器人控制方法研究》和国家“863”高技术计划资助项目《具有环境适应能力的蛇形机器人的研究》为依托，突破以相互抑制机理研究CPG的传统观点，首次创新性地提出应用循环抑制(Cyclic Inhibition, CI)机理来研究蛇形机器人的CPG建模与实现问题。本研究涵概了神经元模型的特性分析、蛇形机器人关节循环抑制CPG建模理论、蛇形机器人循环抑制CPG神经网络稳定性分析以及典型步态的生成方法、循环抑制CPG神经网络控制蛇形机器人蜿蜒运动参数设定策略、应用动力学仿真和实验对该CPG控制方法有效性的验证。 首先，本文介绍了两个用于CPG建模研究的蛇形机器人“勘查者”和“勘查者-I”。给出各自机械系统、控制系统的构成和动力学仿真平台。 其次，详细分析了神经元以及传统的相互抑制(Mutual Inhibition, MI)CPG的特性。从工程角度首次创新性地应用循环抑制建模理论构建了蛇形机器人CPG模型，并对其稳定性进行了深入的分析。首次证明持续型神经元构成的单向循环抑制(Unilateral Cyclic Inhibition, UCI) CPG是能产生振荡输出CPG中微分方程数量最少的，而且其产生振荡输出的机理完全不同于传统的相互抑制CPG。其不需要具备调整功能，只需要神经元之间强的单向循环抑制连接。 第三，首次应用单向激励连接循环抑制CPG构成蛇形机器人神经网络系统。分析了其稳定性，给出其产生振荡输出的条件。通过仿真和实验验证了循环抑制CPG神经网络实现典型步态(蜿蜒运动、伸缩运动和侧向运动)的有效性。首次应用双向循环抑制(Bidirectional Cyclic Inhibition, BCI)CPG神经网络在不同高级控制神经元命令激活下的输出实现蛇形机器人典型运动步态之间的转换。为蛇节律运动生成机制建模提供了新方法。 最后，从实时性、控制方便性等工程应用的角度，对单向循环抑制CPG神经网络实现蛇形机器人蜿蜒运动控制进行了深入的分析。给出了S-波形、幅值、运动速度和运动轨迹曲率的参数设定策略。该系统应用首CPG自激励权重调解成功解决了传统CPG控制系统中CPG的个数比蛇形机器人关节数多一个的问题，并用其实现了一种独特的转弯控制策略。 综上，为蛇形机器人运动控制提供了全新的方法。

Large three-photon absorption and intramolecular charge transfer of the bis-donor fluorene-based molecules

Three-photon absorption (3PA) of two fluorene-based molecules with D-pi-D structural motifs (abbreviated as BPAF and BCZF) has been determined by using a Q-switched Nd: YAG laser pumped with 38 ps pulses at 1064 nm in DMF. The measured 3PA cross-sections are 222 and 140 x 10(-78) cm(6) s(2) for BPAF and BCZF, respectively. AM1 calculations show that attaching different donors changes the charge density distribution of the fluorene skeleton, and it is observed that the 3PA cross-section can be enhanced with increasing intramolecular charge transfer character, measured by the parameter Delta p(1)/Delta p(2)/Delta p(1)'. (c) 2005 Elsevier B.V. All fights reserved.

Theoretical investigation on the one- and two-photon absorption properties for a series of symmetrical charge transfer fluorene-phenylene and fluorene-thiophene derivatives

One- and two-photon absorption properties of a series of fluorene derivatives with symmetrical charge transfer D-IT-D and A-IT-A structural motifs have been theoretically investigated with ZINDO/S method. The optimized structures and the characterization of frontier molecular orbitals were obtained by using AMI calculations. Two-photon absorption properties of molecules have been studied using three-state model. The calculation results have shown that fluorene-thiophene derivatives exhibit larger two-photon absorption cross-section as compared with other studied molecules. To illustrate the results, the crucial effects of thiophene ring on fluorenethiophene derivatives and the net charge changes on the pi-conjugated bridges are analyzed theoretically. (c) 2006 Elsevier B.V. All rights reserved.

Three-photon absorption-induced fluorescence and optical limiting effects in a fluorene derivative

This paper reports on the steady-state fluorescence, three- photon absorption-induced fluorescence emission and subsequently induced optical limiting behaviour of a fluorene derivative with D-pi-D structural motifs. The lifetime of the steady-state fluorescence is 0.903 ns. Large optical limiting behaviour induced by 3PA has also been demonstrated, and the nonlinear absorption coefficient gamma derived from 3PA fitting curves is 5.92 x 10(-20) cm(3)/W-2 and the corresponding molecular 3PA cross-section sigma(3)' is 1.14 x 10(-76) cm(6) s(2).

光周敏感核不育水稻phyA基因的RFLP分析

本文用RFLP方法分析农垦58和光敏核不育水稻农垦58S以及其他一些水稻品种如IR36等，得到如下结果： 1．以第5染色体上8个RFLP标记(RG】3、RG】19、RG470、RG573、RG360、RG403、RG229、RG556)作探针对58和58S进行RFLP分析．没有发现多态性。 2． 58和58S光敏色素(phyA)基因内部（或附近）一些CpG岛的甲基化程度不同。 以IR36 phyA 基因的c DNA克隆作探针，用限制性内切酶EcoRV、Dra I、HindⅢ、Xba工、BglⅡ、Sca工、Msp工对58和58S进行RFLP分析，没有发现多态性，但用HpaII现了多态性。 3．根据IR36 ph yA序列，在5’一非编码区设计一对PCR引物，在IR36、58、58S等水稻品种中均扩出了一段DNA，此DNA片段大小在这几个不同品种中都相同。以此DNA片段（称为PCRI）作探针进行RFLP分析．发现在58S和IR36之间具有多态性，根据测出的58S的PCRI序列以及RFLP分析结果，推测58S和IR36之间的差异是由于插入或缺失引起的。

The mitochondrial genome organization of the rice frog, Fejervarya limnocharis (Amphibia : Anura): a new gene order in the vertebrate mtDNA

The mitochondrial DNA of the rice frog, Fejervarya limnocharis (Amphibia, Anura), was obtained using long-and-accurate polymerase chain reaction (LA-PCR) combining with subcloning method. The complete nucleotide sequence (17,717 bp) of mitochondrial genome was determined subsequently. This mitochondrial genome is characterized by four distinctive features: the translocation of ND5 gene, a cluster of rearranged tRNA genes (tRNA(Thr), tRNA(Pro), tRNA(Leu) ((CUN))) a tandem duplication of tRNA(Mer) gene, and eight large 89-bp tandem repeats in the control region, as well as three short noncoding regions containing two repeated motifs existing in the gene cluster of ND5/tRNA(Thr)/tRNA(Pro)/tRNA(Leu)/tRNA(Phe). The tandem duplication of gene regions followed by deletions of supernumerary genes can be invoked to explain the shuffling of tRNAM(Met) and a cluster of tRNA and ND5 genes, as observed in this study. Both ND5 gene translocation and tandem duplication of tRNA(Met) were first observed in the vertebrate mitochondrial genomes. (c) 2004 Elsevier B.V. All rights reserved.

Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.

Sequence context analysis of 8.2 million single nucleotide polymorphisms in the human genome

We analyzed n-mers (n=3-8) in the local environment of 8,249,446 human SNPs and compared their distribution with that in the genome reference sequences. The results revealed that the short sequences, which contained at least one CpG dinucleotide, occurred

Cardioviral RNA structure logo analysis: entropy, correlations, and prediction

In recent years, there has been an increased number of sequenced RNAs leading to the development of new RNA databases. Thus, predicting RNA structure from multiple alignments is an important issue to understand its function. Since RNA secondary structures are often conserved in evolution, developing methods to identify covariate sites in an alignment can be essential for discovering structural elements. Structure Logo is a technique established on the basis of entropy and mutual information measured to analyze RNA sequences from an alignment. We proposed an efficient Structure Logo approach to analyze conservations and correlations in a set of Cardioviral RNA sequences. The entropy and mutual information content were measured to examine the conservations and correlations, respectively. The conserved secondary structure motifs were predicted on the basis of the conservation and correlation analyses. Our predictive motifs were similar to the ones observed in the viral RNA structure database, and the correlations between bases also corresponded to the secondary structure in the database.

Expression regulation and functional characterization of a novel interferon inducible gene Gig2 and its promoter

Grass carp hemorrhagic virus (GCHV)-induced gene 2 (Gig2) is a novel gene previously identified from UV-inactivated GCHV-treated Carassius auratus blastulae embryonic (CAB) cells, suggesting that it should play a pivotal role in the interferon (IFN) antiviral response. In this study, a polyclonal anti-Gig2 antiserum was generated and used to study the inductive expression pattern by Western blot analysis, showing no basal expression in normal CAB cells but a significant up-regulation upon UV-inactivated GCHV, polyinosinic:polycytidylic acid (Poly I:Q and recombinant IFN (rIFN). However, constitutive expression of Gig2 is observed in all tested tissues from grass carp (Ctenopharyngodon idellus), and Poly I:C injection increases the relative amount of Gig2 protein in skin, spleen, trunk kidney, gill, hindgut and thymus. Moreover, the genomic sequence covering the whole Gig2 ORF and the upstream promoter region were amplified by genomic walking. Significantly, the Gig2 promoter contains three IFN-stimulated response elements (ISREs), nine GAAA/TfTC motifs and five gamma-IFN activating sites (GAS), which are the characteristics of genes responsive to both type I IFN and type 11 IFN. Subsequently, the complete Gig2 promoter sequence was cloned into pGL3-Basic vector, and its activity was measured by luciferase assays in the transfected CAB cells. The Gig2 promoter-driven construct is highly induced in CAB cells after treatment with Poly I:C or rIFN, and the functional capability is dependent on IFN regulatory factor 7 (IRF7), because its activity can be stimulated by IRF7. Collectively, the data provide strong evidence that Gig2 is indeed a novel IFN inducible gene and its expression is likely dependent on IRF7 upon Poly I:C or IFN. (C) 2009 Elsevier Ltd. All rights reserved.